Multiple sequence alignment - TraesCS4D01G187600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G187600 chr4D 100.000 2255 0 0 1 2255 326384560 326382306 0.000000e+00 4165
1 TraesCS4D01G187600 chr4D 96.341 164 6 0 1950 2113 64390634 64390471 1.030000e-68 270
2 TraesCS4D01G187600 chr4B 97.749 2132 45 1 1 2129 406393376 406391245 0.000000e+00 3668
3 TraesCS4D01G187600 chr4B 98.225 338 5 1 1918 2255 406391036 406390700 6.940000e-165 590
4 TraesCS4D01G187600 chr4B 99.057 212 2 0 1918 2129 406391246 406391035 4.540000e-102 381
5 TraesCS4D01G187600 chr4A 92.944 1318 67 9 657 1953 144626098 144627410 0.000000e+00 1895
6 TraesCS4D01G187600 chr5A 87.082 1347 119 28 603 1925 651436632 651437947 0.000000e+00 1472
7 TraesCS4D01G187600 chr5D 85.869 1387 128 35 603 1952 524916967 524918322 0.000000e+00 1413
8 TraesCS4D01G187600 chr5D 97.531 162 4 0 1952 2113 59947682 59947843 6.130000e-71 278
9 TraesCS4D01G187600 chr5D 84.615 130 20 0 621 750 524916700 524916571 1.820000e-26 130
10 TraesCS4D01G187600 chr5B 88.153 996 87 13 603 1592 659411163 659412133 0.000000e+00 1157
11 TraesCS4D01G187600 chr5B 86.731 309 27 7 1590 1897 659412233 659412528 4.640000e-87 331
12 TraesCS4D01G187600 chr3D 96.386 166 6 0 1948 2113 187836304 187836469 7.930000e-70 274
13 TraesCS4D01G187600 chr3A 96.386 166 6 0 1948 2113 238686375 238686210 7.930000e-70 274
14 TraesCS4D01G187600 chr7B 95.266 169 8 0 1945 2113 176002824 176002992 3.690000e-68 268
15 TraesCS4D01G187600 chr7B 95.210 167 8 0 1947 2113 102234312 102234478 4.780000e-67 265
16 TraesCS4D01G187600 chr1B 91.566 83 2 2 592 669 687092560 687092642 2.370000e-20 110


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G187600 chr4D 326382306 326384560 2254 True 4165.000000 4165 100.000000 1 2255 1 chr4D.!!$R2 2254
1 TraesCS4D01G187600 chr4B 406390700 406393376 2676 True 1546.333333 3668 98.343667 1 2255 3 chr4B.!!$R1 2254
2 TraesCS4D01G187600 chr4A 144626098 144627410 1312 False 1895.000000 1895 92.944000 657 1953 1 chr4A.!!$F1 1296
3 TraesCS4D01G187600 chr5A 651436632 651437947 1315 False 1472.000000 1472 87.082000 603 1925 1 chr5A.!!$F1 1322
4 TraesCS4D01G187600 chr5D 524916967 524918322 1355 False 1413.000000 1413 85.869000 603 1952 1 chr5D.!!$F2 1349
5 TraesCS4D01G187600 chr5B 659411163 659412528 1365 False 744.000000 1157 87.442000 603 1897 2 chr5B.!!$F1 1294

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
111 112 0.389817 CGTGGCGTTCTTCTCATGGA 60.390 55.0 0.0 0.0 0.00 3.41 F
442 446 0.761187 AGCACTGCTTCACTCCTTCA 59.239 50.0 0.0 0.0 33.89 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1240 1.271856 TGAATTGCCACTCCCTACGA 58.728 50.0 0.0 0.0 0.0 3.43 R
2232 2781 0.804989 GGCTCCAATGTTCAAGTCCG 59.195 55.0 0.0 0.0 0.0 4.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.051008 ATGTGCTGGTCTGTGAGTGA 58.949 50.000 0.00 0.0 0.00 3.41
49 50 1.204941 GGTCTGTGAGTGATTACGGCT 59.795 52.381 0.00 0.0 0.00 5.52
65 66 2.428925 GCTGGCATGAACCATGGGG 61.429 63.158 18.09 0.9 41.64 4.96
111 112 0.389817 CGTGGCGTTCTTCTCATGGA 60.390 55.000 0.00 0.0 0.00 3.41
118 119 3.189287 GCGTTCTTCTCATGGACAACATT 59.811 43.478 0.00 0.0 37.84 2.71
126 127 3.694926 TCATGGACAACATTGGTATGCA 58.305 40.909 0.00 0.0 37.84 3.96
127 128 3.443329 TCATGGACAACATTGGTATGCAC 59.557 43.478 0.00 0.0 37.84 4.57
128 129 2.868899 TGGACAACATTGGTATGCACA 58.131 42.857 0.00 0.0 35.03 4.57
238 242 1.379146 GGTTCCGGGGCTTCTTCTT 59.621 57.895 0.00 0.0 0.00 2.52
280 284 5.286082 GGTGCTGTTATTTCGTTATTTGCTG 59.714 40.000 0.00 0.0 0.00 4.41
299 303 2.571653 CTGGGTGTTCTTCTGGTATGGA 59.428 50.000 0.00 0.0 0.00 3.41
442 446 0.761187 AGCACTGCTTCACTCCTTCA 59.239 50.000 0.00 0.0 33.89 3.02
569 573 4.824479 TCTTCCACAGCATACAAGATCA 57.176 40.909 0.00 0.0 0.00 2.92
707 711 3.820467 GAGGAAATGTGTTGACCATGTCA 59.180 43.478 0.00 0.0 41.09 3.58
837 846 6.739112 ACTTCAGCCTTAAAATTGAAGACAC 58.261 36.000 20.53 0.0 45.82 3.67
961 972 7.066163 TGCAATTAGTACAATGTTCTCATGAGG 59.934 37.037 22.42 7.8 34.19 3.86
1208 1221 5.776716 AGTGGGTCAATTCTCAAACATCAAT 59.223 36.000 0.00 0.0 0.00 2.57
1227 1240 2.120274 CCCCTTTGCCCCATGTGT 59.880 61.111 0.00 0.0 0.00 3.72
1396 1409 4.608948 ATCAGGATGGTCGGTATCTTTC 57.391 45.455 0.00 0.0 36.16 2.62
1960 2089 6.906848 AGTATATCTAGCATCTACTCCCTCC 58.093 44.000 0.00 0.0 0.00 4.30
1978 2317 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.0 0.00 3.24
2232 2781 2.936202 TCTCTTGCCTGGATAAATGGC 58.064 47.619 0.00 0.0 46.26 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.541147 ACCAGCACATGTTCGATTTGG 59.459 47.619 0.00 0.00 0.00 3.28
41 42 0.034574 TGGTTCATGCCAGCCGTAAT 60.035 50.000 0.00 0.00 33.97 1.89
49 50 1.305129 CACCCCATGGTTCATGCCA 60.305 57.895 11.73 0.00 44.75 4.92
65 66 2.401766 CCTTCAGTGGCCGATGCAC 61.402 63.158 0.00 0.00 40.13 4.57
111 112 3.429492 TCCATGTGCATACCAATGTTGT 58.571 40.909 0.00 0.00 35.38 3.32
118 119 4.206375 CCATAAACTCCATGTGCATACCA 58.794 43.478 0.00 0.00 0.00 3.25
126 127 5.360714 CACTTTATGCCCATAAACTCCATGT 59.639 40.000 8.88 3.37 38.08 3.21
127 128 5.360714 ACACTTTATGCCCATAAACTCCATG 59.639 40.000 8.88 2.87 38.08 3.66
128 129 5.518865 ACACTTTATGCCCATAAACTCCAT 58.481 37.500 8.88 0.00 38.08 3.41
208 212 2.361737 GGAACCAGCTGCTTCCCC 60.362 66.667 24.85 10.44 31.20 4.81
209 213 2.747855 CGGAACCAGCTGCTTCCC 60.748 66.667 27.68 15.91 33.53 3.97
225 229 0.035056 ATCCACAAGAAGAAGCCCCG 60.035 55.000 0.00 0.00 0.00 5.73
280 284 2.838202 TCTCCATACCAGAAGAACACCC 59.162 50.000 0.00 0.00 0.00 4.61
299 303 1.750778 CCAATTGCCGCTTTACCATCT 59.249 47.619 0.00 0.00 0.00 2.90
363 367 6.213525 AGATAGTCCCCCTTCTTTGATTACT 58.786 40.000 0.00 0.00 0.00 2.24
402 406 0.953960 GTCGGGCCAGACAACGAATT 60.954 55.000 28.45 0.00 40.65 2.17
432 436 9.231297 CAAAATTAGGAATAGTTGAAGGAGTGA 57.769 33.333 0.00 0.00 0.00 3.41
477 481 1.139853 GAATGGCTCAAGGAGGACGAT 59.860 52.381 0.00 0.00 0.00 3.73
569 573 6.696411 CAACTCTTATCTCTCAACTGAGGTT 58.304 40.000 6.87 0.00 42.30 3.50
583 587 3.265791 CACCAGGACAGCAACTCTTATC 58.734 50.000 0.00 0.00 0.00 1.75
707 711 4.565652 CCCAACTACTAGCATCCACAAAGT 60.566 45.833 0.00 0.00 0.00 2.66
837 846 7.757097 AGAACACATGTAGTATTAGCTTTCG 57.243 36.000 0.00 0.00 0.00 3.46
1208 1221 2.868566 ACATGGGGCAAAGGGGGA 60.869 61.111 0.00 0.00 0.00 4.81
1227 1240 1.271856 TGAATTGCCACTCCCTACGA 58.728 50.000 0.00 0.00 0.00 3.43
2232 2781 0.804989 GGCTCCAATGTTCAAGTCCG 59.195 55.000 0.00 0.00 0.00 4.79


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.